Proteopedia:Primer

Note for teachers: For teaching purposes, you may copy, adapt and distribute this document. Please remember to replace ‘_YOURSCHOOL’ by some unique identifier for your group, so Sandboxes from other courses will not interfere. Download this Primer as a Word document here.

A Proteopedia Worksheet
1. Getting to know each other:

Access with a web browser http://proteopedia.org. Proteopedia's Main Page should greet you. Take a few minutes to familiarize yourself with the Proteopedia layout.

Proteopedia has a top banner, a left hand side bar and a central area. In turn, the left hand side bar has three sections: from top to bottom: navigation, search, toolbox.

From the navigation area, remember the 'Help' link. It will become handy.

From the toolbox, the 'Export this page' link allows you to save a self-contained version of a fully functional page. Excellent for exporting canned material as lessons that can be displayed even when you don't have internet access.

The search area has two text input boxes. The top one uses Proteopedia's own searching engine and also allows for jumping directly to any page, as long as you enter it's full name. Let's call this input area 'Proteopedia's search'. The bottom text input area uses Google powerful search engine to find pages in Proteopedia related to the word or words you enter. Let's call this bottom text input area 'Google's search'.

2. Logging in Proteopedia:

Proteopedia allows free anonymous access, but editing and creation of pages is only allowed to registered users. To identify yourself to Proteopedia, click on the "Log in/request account" link on the top right hand side of the top banner.

Enter you Username, Password and click 'Log in'. For the purpose of this exercise, your instructor will provide you with a temporary Username and Password. You may also request your own Username by clicking on the "request one" link above the Username input field.

3. Creating your first Proteopedia page:

Type into the Proteopedia's search area the name of the page you want to create. For the purpose of this exercise, enter Sandbox_YOURSCHOOL** (where ** is a unique number you will get from the instructor) and click 'Go'. From now own we'll use the name 'Sandbox_YOURSCHOOL**', but, of course, you will see the name you composed yourself.

Following clicking 'Go', as expected, you will get a message reporting that 'There is no page with the exact title...' and, a little further, a red link 'You can create a page titled Sandbox_YOURSCHOOL**'. Click the red link and Proteopedia will enter into editing mode. You should get a page entitled 'Editing Sandbox_YOURSCHOOL**' and a large central text input area. This is the area where you will enter the text for the page.

A little further down, you see the access link to SAT, the 'Scene authoring tools'. We will use them later on.

Then you will find three buttons: 'Save page', 'Show preview' and 'Show changes', that do exactly what they are named for. You can use 'Show preview' to evaluate the effect of the editing you are working on, and 'Save page' to permanently save the page, in its current state, into Proteopedia's database.

4. Let's start with the page:

For this tutorial, we want to have a clean and fresh page, so please select any text you find in the text input area and delete it, before starting.

Type into the text input area two or three times enter, as to get some empty lines, and then 'Hello World, this is my Proteopedia page' and click 'Show preview'. Now the page will contain under the ‘Editing...' line a preview of your page, with a clear label 'Preview', still displaying the large text input area.

We will now apply some changes on fonts. Scroll down the browser window, back to your edit working area. Use the mouse to select (highlight) the word Proteopedia and click the button with the bold 'B'. Select (highlight) now the words Hello World, and click the button with the slanted I. Click now 'Save page' and behold: your first Proteopedia page is ready.

5. Next, a rotating 3D protein structure:

To enter again the editing mode, simply click the tab [edit this page] located on the top banner. Click in the text input area, to locate the cursor one or two lines below the text you entered before. Note: please be careful when copying words in examples, files name, load= and scene= parameters, and PDB ids are case sensitive.

Click now on the button with the 3D on it. This button inserts a long line, but don't worry about understanding everything in it for now. We want to replace the selected text 'Insert PDB code or filename here' with the PDB id of a structure we'll use for testing, 1acj. Once replaced, the line should start like this '<applet load='1acj' size=...’

Click 'Save page' and observe the result of your work. Your page contains now text and a fully functional Jmol applet, displaying a rotating 3D representation of the protein structure of the Protein Data Bank entry 1ACJ.

Optional: You may enter again editing mode and play a little with the parameters for the &lt;applet line. The value following size= sets the size in pixels for the apple, the text following caption= is the one displayed as caption of the applet, under the rotating structure, the align= parameter can have values left, center, right, and will locate the applet on the page accordingly. Most of the time, align=right is the best option.

6. Now a static image:

To enter again the editing mode, simply click the tab [edit this page] located on the top banner. As before, click in the text input area, to have the cursor located one or two lines below the text you entered. Click now the button with the picture, the sixth from the left. You should get this line, with the word Example.jpg highlighted. You will replace this Example.jpg with the actual name of a sample Image already in Proteopedia: MW_Folding_Simulations.gif

You can also copy and paste the following line:

Click 'Save page' and you will have now both text, image and a 3D representation of 1ACJ.

7. Looking closer to a structure:

We will now start working with the 3D structure.

Enter edit mode and replace the PDB id '1acj' with 'T0499.pdb'. You should have <applet load='T0499.pdb' ... and click 'Save page'. This loads and displays a smaller structure file, previously uploaded to Proteopedia with the 'Upload file' utility under the toolbox in the lower left hand side panel. You may want to also replace the caption text with T0499 ( caption='T0499' ).

Click on 'Save page' and look to the structure. You may click with the mouse over the structure and rotate it. There are several accepted ways of representing and coloring a 3D structure to highlight different aspects related to functionality, structure, elements, etc. The current and default representation is called 'cartoon', where alpha helices are represented as spirals and beta-strands as arrows, pointing from the N to the C terminus.

8. Bringing color to life:

Let's create a link in your page to color the 3D structure with colors that emphasizes the N->C terminus direction on the whole structure, using what's called the GROUP color scheme.

Enter the edit mode with the tab [edit this page], click in the text input area, to have the cursor located one or two lines below the text you entered, copy the following line and click 'Save page'

N to C terminus

Your page should have now a green link, able to interact with the Jmol applet. Click on it. The 3D model should display a rainbow coloring, from dark blue signaling the N-terminal (start of the chain) to the C-terminal (end of the chain).

Edit your page again, type this line below the previous one, and save.

structure

By clicking on this new link, you can distinguish clearly the two main types of secondary structure in this model: alpha helix and beta strand. This schema uses six different colors to distinguish four types of protein secondary structures (helices, beta strands and sheets, turns, and loops) and DNA vs. RNA.

9. Adding some explanations to the page:

Proteopedia's green links are much like the standard links on a HTML page, where you frame a word with a start/end tag to make it 'hot' and responsive to a mouse click. Try to enter some explanation around the last link you created. Enter the edit mode, and type some text before and after the line structure and click 'Save page'. here's a suggestion:

Let us color the two main forms of regular secondary structure in this protein. Alpha helix appears in red, beta sheet in yellow.

10. Quiz anyone?

Now, we will create a simple quiz for self-evaluation. Enter the edit mode, click in the text input area, to have the cursor located one or two lines below the text you entered and copy these lines:

{How many alpha helices are in this structure? - None. + One. - Four.
 * type="[]"}

Save the page and have fun by testing it. More possibilities are explained at Help:Quiz.

11. This is the END.

This marks the end of this exercise. With it, you should be able to create a Proteopedia page with text, static images and 3D models of protein structures. You should be able to interact with the model and create quizzes for student evaluation.

A more complete description is available on Proteopedia.org, by clicking the 'Help' link on the top left hand-side of the screen.

12. … and beyond, the real fun:

How to create your own scenes: The Scene Authoring Tool (SAT) is a unique and powerful Proteopedia feature for easily creating 3D scenes. The files ‘colorGROUP’ and ‘colorSTRUCTURE’ you used during the exercise, are examples of simple scenes. To create a slightly complicated one, open on a separated web browser page Proteopedia.org, click on ‘Help’ (top left) and then click on ‘Proteopedia:DIY:Scenes’.

On your page, enter the edit mode with the tab [edit this page], click in the text input area, to have the cursor located one or two lines below the text you entered, click on the ‘3D’ button and type 1acj where the selected text states 'Insert PDB code or filename here'.

Click on [show] Scene authoring tools (SAT), and follow the step-by-step instructions on the Tacrine section of the Proteopedia:DIY:Scenes page.

An annotated applet: The line ‘<Structure…’ created when you click on the button 3D provides enough support for displaying a rotating 3D structure and interact with it.

You may also want to display an applet with complete Functional, Evolutionary and Structural information of a PDB file. The following line shows how.

Enter this line and replace ‘1acj’ with the PDB id you want to display. Automatic data mining processes weekly refresh the added information.